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  • Title: Guidelines for reproducible analysis of adaptive immune receptor repertoire sequencing data.
    Author: Peres A, Klein V, Frankel B, Lees W, Polak P, Meehan M, Rocha A, Correia Lopes J, Yaari G.
    Journal: Brief Bioinform; 2024 Mar 27; 25(3):. PubMed ID: 38752856.
    Abstract:
    Enhancing the reproducibility and comprehension of adaptive immune receptor repertoire sequencing (AIRR-seq) data analysis is critical for scientific progress. This study presents guidelines for reproducible AIRR-seq data analysis, and a collection of ready-to-use pipelines with comprehensive documentation. To this end, ten common pipelines were implemented using ViaFoundry, a user-friendly interface for pipeline management and automation. This is accompanied by versioned containers, documentation and archiving capabilities. The automation of pre-processing analysis steps and the ability to modify pipeline parameters according to specific research needs are emphasized. AIRR-seq data analysis is highly sensitive to varying parameters and setups; using the guidelines presented here, the ability to reproduce previously published results is demonstrated. This work promotes transparency, reproducibility, and collaboration in AIRR-seq data analysis, serving as a model for handling and documenting bioinformatics pipelines in other research domains.
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